Welcome to ChromBERT-tools

ChromBERT-tools is a lightweight toolkit built on top of the ChromBERT foundation model. It helps users generate, model, and interpret context-specific regulatory representations from their own genomic data through command-line interfaces (CLIs) and Python APIs.

ChromBERT is a pre-trained foundation model designed to capture genome-wide co-association patterns among transcription regulators and to learn context-specific transcriptional regulatory networks.

ChromBERT-tools framework

Key features

  • Simple interface — provides a single chrombert-tools entry point with composable subcommands.

  • Human and mouse support — supports hg38 and mm10 genomes at multiple resolutions.

  • Modular workflows — supports representation generation, predictive modeling, and regulatory interpretation.

  • Cell-type-specific analysis — supports context-specific analyses using accessibility tracks or fine-tuned checkpoints.

  • CLI and Python API — exposes core functions through both shell commands and importable Python APIs.

Core functionality

ChromBERT-tools is organized into three functional layers:

  • Representation generation — generate context-specific representations for genomic regions or regulators.

  • Predictive modeling — train or apply models for region classification, region activity prediction, and gene activity prediction.

  • Regulatory interpretation — infer functional relationships among regions, regulators, and regulatory programs.

It also provides end-to-end application workflows for common biological tasks, including cell-type-specific key regulator identification, driver regulator identification during cell-state transitions, context-specific cofactor analysis, and TF-binding prediction.

Getting started

  1. Follow Installation to install ChromBERT-tools using the recommended Apptainer image or from source.

  2. Download the required ChromBERT model and annotation files using download-data.

  3. See Usage for the full list of available commands and tutorials.

To list all available commands:

chrombert-tools --help

To get help for a specific command:

chrombert-tools <command> --help

User guide

User Guide

Contact

For questions or suggestions, please contact us at 2211083@tongji.edu.cn.

Indices and tables